The genome sequence of <i>Samia ricini</i>, a new model species of lepidopteran insect

Lee, Jung; Nishiyama, Tomoaki; Shigenobu, Shuji; Yamaguchi, Katsushi; Suzuki, Yutaka; Shimada, Toru; Katsuma, Susumu; Kiuchi, Takashi

doi:10.1111/1755-0998.13259

Cited by 17 publications

(8 citation statements)

References 70 publications

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“…Long interspersed nuclear elements (LINEs) are the second most abundant repeat category with >39 million bases (7.23%), followed by DNA transposons and rolling circles and long terminal repeats (LTRs), which have >15 million (2.82%) and >11 million bases (2.10%) respectively. Percent composition of repeats and predominance of LINEs were similar to both the S. ricini and Bombyx mori genome assemblies ( Lee et al 2021 ).…”

Section: Resultssupporting

confidence: 52%

First Annotated Genome of a Mandibulate Moth, Neomicropteryx cornuta, Generated Using PacBio HiFi Sequencing

Ellis

Plotkin

et al. 2021

Genome Biology and Evolution

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We provide a new, annotated genome assembly of Neomicropteryx cornuta, a species of the so-called “mandibulate archaic moths” (Lepidoptera: Micropterigidae). These moths belong to a lineage that is thought to have split from all other Lepidoptera more than 300 million years ago and are consequently vital to understanding the early evolution of superorder Amphiesmenoptera, which contains the order Lepidoptera (butterflies and moths) and its sister order Trichoptera (caddisflies). Using PacBio HiFi sequencing reads, we assembled a highly-contiguous genome with a contig N50 of nearly 17 Mbp. The assembled genome length of 541,115,538 bp is about half the length of the largest published Amphiesmenoptera genome (Limnephilus lunatus, Trichoptera) and double the length of the smallest (Papilio polytes, Lepidoptera). We find high recovery of universal single copy orthologs with 98.1% of BUSCO genes present and provide a genome annotation of 15,643 genes aided by resolved isoforms from PacBio IsoSeq data. This high-quality genome assembly provides an important resource for studying ecological and evolutionary transitions in the early evolution of Amphiesmenoptera.

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Section: Resultssupporting

confidence: 52%

First Annotated Genome of a Mandibulate Moth, Neomicropteryx cornuta, Generated Using PacBio HiFi Sequencing

Ellis

Plotkin

et al. 2021

Genome Biology and Evolution

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“…We compared the accuracy of TSEBRA with EVM, one of the most cited combiner tools to date. EVM was previously used to combine BRAKER with other predictions [ 41 ], to combine BRAKER2 predictions with RNA-seq evidence [ 42 , 43 ] or other RNA-seq based predictions [ 44 ], and even for combining multiple BRAKER predictions [ 45 ]. Still, it is not the most suitable task for EVM to create a BRAKER-only combination.…”

Section: Resultsmentioning

confidence: 99%

TSEBRA: transcript selector for BRAKER

et al. 2021

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Background BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains statistical models of protein-coding genes based on provided evidence and, then predicts protein-coding genes in genomic sequences using both the extrinsic evidence and statistical models. For training and prediction, BRAKER1 and BRAKER2 incorporate complementary extrinsic evidence: BRAKER1 uses only RNA-seq data while BRAKER2 uses only a database of cross-species proteins. The BRAKER suite has so far not been able to reliably exceed the accuracy of BRAKER1 and BRAKER2 when incorporating both types of evidence simultaneously. Currently, for a novel genome project where both RNA-seq and protein data are available, the best option is to run both pipelines independently, and to pick one, likely better output. Therefore, one or another type of the extrinsic evidence would remain unexploited. Results We present TSEBRA, a software that selects gene predictions (transcripts) from the sets generated by BRAKER1 and BRAKER2. TSEBRA uses a set of rules to compare scores of overlapping transcripts based on their support by RNA-seq and homologous protein evidence. We show in computational experiments on genomes of 11 species that TSEBRA achieves higher accuracy than either BRAKER1 or BRAKER2 running alone and that TSEBRA compares favorably with the combiner tool EVidenceModeler. Conclusion TSEBRA is an easy-to-use and fast software tool. It can be used in concert with the BRAKER pipeline to generate a gene prediction set supported by both RNA-seq and homologous protein evidence.

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“…A total of 155 scaffolds of S. ricini genome assembly ( 44 ), 171 159 de novo assemblies of RNA-seq reads, 78 839 ORFs predicted from RNA-seq assemblies and 20 320 cDNA ends ( 41 ) were installed. The RNA-seq assemblies and predicted ORFs were annotated with GO terms, blast results against nr and their transcript levels (RNA-seq assemblies only).…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, S. ricini (Eri silkmoth), a gigantic and polyphagous saturniid moth, is the almost fully domesticated saturniid species. The genome sequence of these species was recently determined by our collaborators ( 44 ).…”

Section: Resultsmentioning

confidence: 99%

SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species

2022

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We introduce SilkBase as an integrated database for transcriptomic and genomic resources of the domesticated silkworm Bombyx mori and related species. SilkBase is the oldest B. mori database that was originally established as the expressed sequence tag database since 1999. Here, we upgraded the database by including the datasets of the newly assembled B. mori complete genome sequence, predicted gene models, bacterial artificial chromosome (BAC)-end and fosmid-end sequences, complementary DNA (cDNA) reads from 69 libraries, RNA-seq data from 10 libraries, PIWI-interacting RNAs (piRNAs) from 13 libraries, ChIP-seq data of 9 histone modifications and HP1 proteins and transcriptome and/or genome data of four B. mori-related species, i.e. Bombyx mandarina, Trilocha varians, Ernolatia moorei and Samia ricini. Our new integrated genome browser easily provides a snapshot of tissue- and stage-specific gene expression, alternative splicing, production of piRNAs and histone modifications at the gene locus of interest. Moreover, SilkBase is useful for performing comparative studies among five closely related lepidopteran insects. Database URL: https://silkbase.ab.a.u-tokyo.ac.jp

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The genome sequence of Samia ricini, a new model species of lepidopteran insect

Cited by 17 publications

References 70 publications

First Annotated Genome of a Mandibulate Moth, Neomicropteryx cornuta, Generated Using PacBio HiFi Sequencing

First Annotated Genome of a Mandibulate Moth, Neomicropteryx cornuta, Generated Using PacBio HiFi Sequencing

TSEBRA: transcript selector for BRAKER

SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species

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